Abstract
Barred galaxias, Galaxias fuscus, is an endangered freshwater fish confined to headwaters of mountain streams in the Goulburn River system in central Victoria, Australia. Next generation DNA sequencing was used to develop a suite of microsatellite markers that can be used for future population genetic assessments of G. fuscus. A total of 24 polymorphic loci were identified and 12 characterized using 30 individuals from a single sample locale. We observed low to moderate genetic variation across most loci (mean number of alleles per locus = 2.58; mean expected heterozygosity = 0.37) with no evidence of individual loci deviating significantly from Hardy–Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. The 12 markers characterized in the present study provide a valuable resource for future population genetic assessments and management of G. fuscus in Australia.
This is a preview of subscription content, log in via an institution to check access.
References
Blacket MJ, Robin C, Good RT, Lee SF, Miller AD (2012) Universal primers for fluorescent labelling of 1 PCR fragments—an efficient and cost effective approach to genotyping by fluorescence. Mol Ecol Notes. doi:10.1111/j.1755-0998.2011.03104.x
Brookfield JFY (1996) A simple new method for estimating null allele frequency from heterozygote deficiency. Mol Ecol 5:453–455
Mack G (1936) Victorian species of the genus Galaxias, with descriptions of two new species. Mem Natl Mus Vic 9:98–101
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380
Meglécz E, Costedoat C, Dubut V, Gilles A, Malausa T, Pech N, Martin JF (2010) QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects. Bioinformatics 26(3):403–404
Park SDE (2001) Trypanotolerance in West African Cattle and the population genetic effects of selection. PhD Thesis, University of Dublin
Raadik TA, Faribrother PS, Smith SJ (2010) National recovery plan for the Barred Galaxias, Galaxias fuscus. Department of Sustainability and Environment, Victoria, Australia. http://www.environment.gov.au/biodiversity/threatened/publications/recovery/pubs/barred-galaxias.pdf
Raymond M, Rousset F (1995) An exact test for population differentiation. Evolution 49:1280–1283
Rice WR (1989) Analyzing tables of statistical tests. Evolution 43(1):223–225
Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386
Van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4(3):535–538
Acknowledgments
The authors thank Michael Nicol, Dean Hartwell and Graeme Seppings for help with sample collection. This project was funded through the Commonwealth Caring for Our Country program and the Victorian and Commonwealth government’s Statewide Bushfire Recovery Plan, and was conducted under the Fisheries Act 1995 permit RP827, National Parks Act 1975 and Flora and Fauna Guarantee Act 1988 permit 10005451 and animal ethics permit AEC07/24.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Miller, A.D., van Rooyen, A., Ayres, R.M. et al. The development of 24 polymorphic microsatellite loci for the endangered barred galaxias, Galaxias fuscus, through next generation DNA sequencing. Conservation Genet Resour 4, 613–616 (2012). https://doi.org/10.1007/s12686-012-9605-x
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12686-012-9605-x